Plants are constantly exposed to microbial attacks and have developed sophisticated systems to counteract them. Plants respond to infection using a two-branched innate immune system [1]: a first branch, called basal resistance, responds to pathogen-associated molecular patterns (PAMPs). Basal resistance is thought to be the default defense system that allows limited restriction of pathogen growth. A second branch, called gene-for-gene resistance, responds to pathogen virulence factors. Both basal and the gene-for-gene induced resistances can be divided into three steps.
In a first step, the plant throughout different recognition systems detects PAMP or virulence effectors of the pathogen; these recognition systems involve pattern recognition receptors (PRRs) for basal resistance and resistance (R) genes for gene-for-gene resistance [1, 2]. In rice, the transmembrane glycoprotein CEBiP is the best-characterized example of PRR for basal resistance to the fungal pathogen Magnaporthe oryzae [3]. There is little polymorphism in the case of PRR and in the molecular pattern that they recognize. The gene-for-gene recognition system is much more polymorphic. Depending on the presence/absence of the R genes and of the corresponding pathogen molecule, the interaction will be incompatible (plant is resistant) or compatible (plant is susceptible).
In a second step, signal transduction occurs and requires regulators such as MAP kinases [4] and transcription factors [5]. These genes that are here collectively called defense regulators are often conserved across species; for example NPR1 is a central regulator in both Monocots and Dicots [6, 7, 8, 9, 10]. Many of these regulator genes are differentially expressed during infection [11, 12].
In a third step, defense responses are induced. These include production of antimicrobial secondary metabolites (phytoalexins) [13], pathogenesis-related (PR) proteins (e.g. chitinases, glucanases) [14, 15], cell-wall strengthening [16] and programmed cell death, leading to the Hypersensitive Response (HR) [17]. The genes that act downstream of the regulators controlling the disease resistance pathways are collectively called defense genes and are typically transcriptionally regulated upon infection.
Besides these mechanisms explaining how resistance is built, breeders and biologists use an agnostic but operational term for a phenomenon found in many plant species: partial resistance. Partial resistance is first characterized by quantitative limitation of pathogen growth. In rice, partial resistance to the blast fungus M. oryzae is often divided into two main values: the number and the size of lesions [18]. Another characteristic of partial resistance is that it is controlled by the plant development and usually increases with aging [19]. Rice is a good model to study partial resistance as breeders have extensively used it, through the identification of quantitative trait loci (QTL). There is a considerable amount of genetic data available that was recently reviewed [18]. More than 340 QTL have been identified and summarized to 165 metaQTLs. Further analysis lead to the identification of an operational set of about 20 genomic areas. Importantly, this large set of genetic data could be compared to the large set of information available on R gene analogs, regulators and defense genes in rice [12, 18]. This analysis showed that, on a global scale, R gene analogs are often found in intervals defining metaQTLs [18]. This was an expected finding consistent with the hypothesis that partial resistance is due, in part, to defective R genes that recognize with low efficiency pathogens and trigger weak defense response. Less expected was the finding that regulator and some defense genes were also significantly associated with metaQTLs [12]. Finally, partial resistance has long been considered as a durable form of resistance. This may be due to the fact that the low levels of resistance conferred by partial resistance do not impose strong selection pressure for the pathogens. This may also be due to particular mechanisms that cannot be easily broken down by pathogens.
Preformed, constitutive, physical and chemical barriers likely play a role in partial resistance by limiting the growth of a normally virulent pathogen. They involve cuticle [20] and cell wall strengthening [21] and represent mostly broad-spectrum pathogen resistance. In rice, like in other plants, silicon accumulation plays direct and indirect role in partial resistance [22]. Antimicrobial molecules, called phytoanticipins, can also accumulate before infection [23]. Although there is a large body of evidence that defense genes, especially pathogenesis-related (PR) proteins, are constitutively expressed in uninfected tissues [15], there is no indication of the effect of their level of expression before infection on resistance. In contrast, there are many indications that the over-production of PR proteins confers resistance [24, 25], that mutations in genes negatively regulating disease resistance can increase defense gene expression [e.g. 26, 27] or that over-expression of regulator genes acting positively on disease resistance can increase defense gene expression [e.g. 28]. Thus there are indirect evidences that constitutive expression of regulator and defense genes could participate to plant pathogen resistance.
To face pathogen attacks, plants could use a proactive strategy of constitutive expression of inducible defense systems. Recently, large-scale expression studies across Arabidopsis thaliana cultivars have been completed and showed that gene expression greatly vary from one genotype to another [29]. Interestingly, the 2,200 differentially expressed genes were significantly enriched for genes classified as controlling biotic and abiotic responses [29]. Thus these classes of genes seem to display high expression level polymorphism (ELP). However, there is little information of a possible link between these ELPs and biological traits. ELP of major R genes can obviously explain the polymorphism in the disease resistance pathway [30, 31]. In these cases, the presence/absence of the resistant R allele explains the ELP and the corresponding resistance/susceptibility phenotypes. In the case of partial resistance, there is no evidence that plants show ELPs of the surveillance receptors and/or regulator and defense systems. Our hypothesis is that such expression level polymorphism for receptors, regulator and defense genes belonging to plant disease resistance pathways play a role in partial resistance.
We wanted to test the hypothesis that, besides inducible defense systems, rice has developed a proactive strategy to face its major fungal pathogen, M. oryzae. For this purpose, we looked for possible links between constitutive levels of expression of genes markers of the disease resistance pathways (thereafter called defense-related genes) in relation to partial resistance. We show that constitutive expression of defense-related genes shows high ELP and likely plays a central role in partial resistance to M. oryzae. Thus we identify a possible mechanism underlying a phenomenon that has been known and used for a long time with no comprehensive knowledge of what was behind.